Changeset 1010

Timestamp:

Oct 28, 2010, 4:39:45 PM (13 years ago)

Author:

j.saito@…

Message:

Ticket #57 - Unified getAssays and getAssay.

Also, added convenience method for checking the params object in RestControllers? in CommunicationManager?.

Location:

trunk

Files:

• grails-app/controllers/RestController.groovy (modified) (5 diffs)
• src/groovy/dbnp/rest/common/CommunicationManager.groovy (modified) (2 diffs)

trunk/grails-app/controllers/RestController.groovy

@@ -21 +21 @@
 import grails.converters.*
 import nl.metabolomicscentre.dsp.http.BasicAuthentication
+import dbnp.rest.common.CommunicationManager
 
 
@@ -32 +33 @@
         def beforeInterceptor = [action:this.&auth,except:["isUser"]]
         def credentials
-        def requestUser // = SecUser.findByName( "user" )
+        def requestUser //= SecUser.findByUsername( "user" )
 
         /**
@@ -139 +140 @@
          * If the user is not allowed to read the study contents, a 401 error is given
          *
-         * Example call of the getAssays REST resource:
-         * http://localhost:8080/gscf/rest/getAssays?studyToken=PPSH&moduleURL=http://localhost:8182/sam
-         *
          * @param       studyToken      String The external study id (code) of the target GSCF Study object
          * @param       moduleURL       String The base URL of the calling dbNP module
          * @param       consumer        consumer name of the calling module
-         * @param       token           token for the authenticated user (e.g. session_id)
          * @return list of assays in the study as JSON object list, filtered to only contain assays
          *         for the specified module, with 'assayToken' and 'name' for each assay
+         *
+         *
+         * Example 1. REST call without assayToken 
+         *            http://localhost:8080/gscf/rest/getAssays/aas?studyToken=PPSH
+         *                              &moduleURL=http://localhost:8182/sam
+         *
+         * Result: [{"name":"Glucose assay after",
+         *                      "module":{"class":"dbnp.studycapturing.AssayModule","id":1,"name":"SAM module for clinical data",
+         *                              "platform":"clinical measurements","url":"http://localhost:8182/sam"},
+         *                      "externalAssayID":"PPSH-Glu-A", "Description":null,"parentStudyToken":"PPSH"},
+         *                      {"name":"Glucose assay before",
+         *                              "module":{"class":"dbnp.studycapturing.AssayModule","id":1,"name":"SAM module for clinical data",
+         *                              "platform":"clinical measurements","url":"http://localhost:8182/sam"},
+         *                              "externalAssayID":"PPSH-Glu-B","Description":null,"parentStudyToken":"PPSH"}]
+         *
+         *
+         * Example 2. REST call with one assayToken 
+         *                        http://localhost:8080/gscf/rest/getAssays/queryOneTokenz?studyToken=PPSH
+         *                              &moduleURL=http://localhost:8182/sam&assayToken=PPSH-Glu-A
+         *
+         * Result: [{"name":"Glucose assay after","module":{"class":"dbnp.studycapturing.AssayModule","id":1,
+         *                      "name":"SAM module for clinical data","platform":"clinical measurements","url":"http://localhost:8182/sam"},
+         *                      "externalAssayID":"PPSH-Glu-A","Description":null,"parentStudyToken":"PPSH"}]
+         *
+         *
+         * Example 3. REST call with two assayTokens.
+         *
+         * Result: Same as result in Example 1.
          */
         def getAssays = {
-                List assays = [] 
+
+                List returnList = []    // return list of hashes each containing fields and values belonging to an assay 
+
+                // Check if required parameters are present 
+                def validCall = CommunicationManager.hasValidParams( params, "moduleURL", "studyToken" )
+                if( !validCall ) { 
+                        render "Error. Wrong or insufficient parameters." as JSON 
+                        return
+                }
+
                 if( params.studyToken ) {
+
                         def id = params.studyToken
                         def study = Study.find( "from Study as s where s.code=?", [id] )
@@ -162 +197 @@
                                 }
 
-                                study.assays.each{ assay ->
+                                def assays = []
+                                if(params.assayToken==null) {
+                                        assays = study.assays
+                                }
+                                else if( params.assayToken instanceof String ) { 
+                                        def assay = study.assays.find{ it.externalAssayID==params.assayToken }
+                                        if( assay ) {
+                                                 assays.push assay
+                                        }
+                                }
+                                else {                                                                                                  // there are multiple assayTokens instances
+                                        params.assayToken.each { assayToken ->
+                                                def assay = study.assays.find{ it.externalAssayID==assayToken }
+                                                if(assay) {
+                                                        assays.push assay
+                                                }
+                                        }
+                                }
+
+                                assays.each{ assay ->
                                         if (assay.module.url.equals(params.moduleURL)) {
-                                                def map = ['name':assay.name, 'assayToken':assay.getToken()]
-                                                assays.push( map )
+                                                if(assay) {
+                                                        def map = [:]
+                                                        assay.giveFields().each { field ->
+                                                                def name = field.name
+                                                                def value = assay.getFieldValue( name )
+                                                                if(field.name=='externalAssayID') {
+                                                                        name = 'assayToken'
+                                                                }
+                                                                map[name] = value
+                                                        }
+                                                        map["parentStudyToken"] = assay.parent.getToken()
+                                                        returnList.push( map )
+                                                }
                                         }
                                 }
-                        }
+                }
+
                 }
-                render assays as JSON 
-        }
+
+                render returnList as JSON 
+        }
+
+
+
+
+
+
 
         /**
@@ -310 +383 @@
 
 
-        /**
-         * REST resource for dbNP modules.
-         *
-         * @param       assayToken String, the external identifier of the study
-         * @param       consumer        consumer name of the calling module
-         * @param       token           token for the authenticated user (e.g. session_id)
-         * @return List of all fields of this assay
-         *
-         * Example REST call (without authentication):
-     * http://localhost:8080/gscf/rest/getAssay/assay?assayToken=PPS3_SAM
-     *
-         * Returns the JSON object: {"name":"Lipid profiling","module":{"class":"dbnp.studycapturing.AssayModule","id":1,
-         * "name":"SAM module for clinical data","platform":"clinical measurements","url":"http://sam.nmcdsp.org"},
-         * "assayToken":"PPS3_SAM","parentStudyToken":"PPS","Description":null}
-         */
-        def getAssay = {
-                def items = [:]
-                if( params.assayToken ) {
-                        def assay = Assay.find( "from Assay as a where externalAssayID=?",[params.assayToken])
-                        if(assay) {
-                                assay.giveFields().each { field ->
-                                        def name = field.name
-                                        def value = assay.getFieldValue( name )
-                                        items[name] = value
-                                }
-                                items["parentStudyToken"] = assay.parent.getToken()
-                        }
-        }
-                render items as JSON
-        }
-
-
 
         /**

trunk/src/groovy/dbnp/rest/common/CommunicationManager.groovy

@@ -4 +4 @@
 import java.net.URLEncoder
 import org.codehaus.groovy.grails.web.json.*
+
 
 /**  CommunicationManager
@@ -264 +265 @@
 
 
+    /**
+     * Give list of missing parameters for a parameter call in a RestController.
+     *  
+     * @params params Map params        The parameter list required by this view.
+     * @params requiredParamers                 List of parameter names that must be provided
+     * @return true, if params has all required parameters, false otherwise 
+     */  
+        static String hasValidParams( params, Object [] requiredParams ) {
+                def list = []
+                requiredParams.each { p ->
+                        if( !params[p] ) list.push p
+                }
+                if(list.size()>0) { return true }
+                return false
+        }
+
+
 
 }